Biological samples can be imaged using a microscope. Many biological samples include three-dimensional structures, and imaging the structures in three dimensions can provide additional information about the structure. A three-dimensional structure includes planes that are at different depths within the structure. Changing the position of the sample relative to an objective lens of the microscope can bring each plane in the structure into focus at a different time. In this manner, a three-dimensional image of the structure can be built up over a period of time from the images of the individual planes.